Merge remote-tracking branch 'nipy/master' into clean-afni

Author: tsalo

CHANGES

@@ -1,7 +1,7 @@
 Upcoming release 0.13
 =====================
 
-* REF: Refactor AFNI interfaces (https://github.com/nipy/nipype/pull/1678)
+* REF: Refactor AFNI interfaces (https://github.com/nipy/nipype/pull/1678, https://github.com/nipy/nipype/pull/1680)
 * ENH: Move nipype commands to group command using click (https://github.com/nipy/nipype/pull/1608)
 * FIX: AFNI Retroicor interface fixes (https://github.com/nipy/nipype/pull/1669)
 * FIX: Minor errors after migration to setuptools (https://github.com/nipy/nipype/pull/1671)

nipype/algorithms/confounds.py

@@ -281,10 +281,9 @@ def _list_outputs(self):
 class CompCorInputSpec(BaseInterfaceInputSpec):
     realigned_file = File(exists=True, mandatory=True,
                           desc='already realigned brain image (4D)')
-    mask_file = File(exists=True, mandatory=False,
-                     desc='mask file that determines ROI (3D)')
+    mask_file = File(exists=True, desc='mask file that determines ROI (3D)')
     components_file = File('components_file.txt', exists=False,
-                           mandatory=False, usedefault=True,
+                           usedefault=True,
                            desc='filename to store physiological components')
     num_components = traits.Int(6, usedefault=True) # 6 for BOLD, 4 for ASL
     use_regress_poly = traits.Bool(True, usedefault=True,

nipype/algorithms/tests/test_auto_TCompCor.py

@@ -4,14 +4,12 @@
 
 
 def test_TCompCor_inputs():
-    input_map = dict(components_file=dict(mandatory=False,
-    usedefault=True,
+    input_map = dict(components_file=dict(usedefault=True,
     ),
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
-    mask_file=dict(mandatory=False,
-    ),
+    mask_file=dict(),
     num_components=dict(usedefault=True,
     ),
     percentile_threshold=dict(usedefault=True,

nipype/interfaces/nilearn.py

@@ -37,20 +37,19 @@ class SignalExtractionInputSpec(BaseInterfaceInputSpec):
                                'corresponds to the class labels in label_file '
                                'in ascending order')
     out_file = File('signals.tsv', usedefault=True, exists=False,
-                    mandatory=False, desc='The name of the file to output to. '
+                    desc='The name of the file to output to. '
                     'signals.tsv by default')
-    incl_shared_variance = traits.Bool(True, usedefault=True, mandatory=False, desc='By default '
+    incl_shared_variance = traits.Bool(True, usedefault=True, desc='By default '
                                        '(True), returns simple time series calculated from each '
                                        'region independently (e.g., for noise regression). If '
                                        'False, returns unique signals for each region, discarding '
                                        'shared variance (e.g., for connectivity. Only has effect '
                                        'with 4D probability maps.')
-    include_global = traits.Bool(False, usedefault=True, mandatory=False,
+    include_global = traits.Bool(False, usedefault=True,
                                  desc='If True, include an extra column '
                                  'labeled "global", with values calculated from the entire brain '
                                  '(instead of just regions).')
-    detrend = traits.Bool(False, usedefault=True, mandatory=False,
-                          desc='If True, perform detrending using nilearn.')
+    detrend = traits.Bool(False, usedefault=True, desc='If True, perform detrending using nilearn.')
 
 class SignalExtractionOutputSpec(TraitedSpec):
     out_file = File(exists=True, desc='tsv file containing the computed '

nipype/interfaces/tests/test_auto_SignalExtraction.py

@@ -6,24 +6,20 @@
 def test_SignalExtraction_inputs():
     input_map = dict(class_labels=dict(mandatory=True,
     ),
-    detrend=dict(mandatory=False,
-    usedefault=True,
+    detrend=dict(usedefault=True,
     ),
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
     in_file=dict(mandatory=True,
     ),
-    incl_shared_variance=dict(mandatory=False,
-    usedefault=True,
+    incl_shared_variance=dict(usedefault=True,
     ),
-    include_global=dict(mandatory=False,
-    usedefault=True,
+    include_global=dict(usedefault=True,
     ),
     label_files=dict(mandatory=True,
     ),
-    out_file=dict(mandatory=False,
-    usedefault=True,
+    out_file=dict(usedefault=True,
     ),
     )
     inputs = SignalExtraction.input_spec()